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An Information Portal to 105025 Biological Macromolecular Structures

X-RAY DIFFRACTION
Materials and Methods page
3V4D
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 4
    Temperature 293.0
    Details 0.1 M MMT, 30% PEG 1500, +xylitol, K/Na tartrate, 2,6-pyridinecarboxylic acid, 2,4-pyridinecarboxylic acid, 2,5-pyridinecarboxylic acid, 4-pyridazine carboxylic acid, 3-sulfobenzoic acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 92.25 α = 90
    b = 179.18 β = 90
    c = 45.22 γ = 90
     
    Space Group
    Space Group Name:    P 21 21 2
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type MARMOSAIC 225 mm CCD
    Collection Date 2010-11-12
     
    Diffraction Radiation
    Monochromator C (111)
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type APS BEAMLINE 21-ID-F
    Wavelength List 0.9787
    Site APS
    Beamline 21-ID-F
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) -3.0
    Resolution(High) 1.95
    Resolution(Low) 50
    Number Reflections(All) 55593
    Number Reflections(Observed) 55593
    Percent Possible(Observed) 99.9
    R Merge I(Observed) 0.094
    B(Isotropic) From Wilson Plot 28.6
    Redundancy 9.6
     
    High Resolution Shell Details
    Resolution(High) 1.95
    Resolution(Low) 1.98
    Percent Possible(All) 100.0
    R Merge I(Observed) 0.633
    Mean I Over Sigma(Observed) 3.0
    R-Sym I(Observed) 0.633
    Redundancy 9.0
    Number Unique Reflections(All) 2712
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method SAD
    reflnsShellList 1.95
    Resolution(Low) 50.0
    Cut-off Sigma(I) 0.0
    Cut-off Sigma(F) 0.0
    Number of Reflections(all) 52607
    Number of Reflections(Observed) 52607
    Number of Reflections(R-Free) 2816
    Percent Reflections(Observed) 99.69
    R-Factor(All) 0.1946
    R-Factor(Observed) 0.1946
    R-Work 0.19337
    R-Free 0.21658
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 43.366
    Anisotropic B[1][1] -0.43
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -3.17
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 3.6
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 1.952
    Shell Resolution(Low) 2.002
    Number of Reflections(R-Free) 191
    Number of Reflections(R-Work) 3515
    R-Factor(R-Work) 0.26
    R-Factor(R-Free) 0.281
    Percent Reflections(Observed) 99.28
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    r_gen_planes_other 0.008
    r_gen_planes_refined 0.01
    r_chiral_restr 0.104
    r_dihedral_angle_4_deg 14.983
    r_dihedral_angle_3_deg 12.056
    r_dihedral_angle_2_deg 28.923
    r_dihedral_angle_1_deg 6.543
    r_angle_other_deg 2.395
    r_angle_refined_deg 1.707
    r_bond_other_d 0.006
    r_bond_refined_d 0.018
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 5642
    Nucleic Acid Atoms 0
    Heterogen Atoms 0
    Solvent Atoms 342
     
     
  •   Software and Computing Hide
    Computing
    Data Collection MD2
    Data Reduction (intensity integration) HKL-2000
    Data Reduction (data scaling) HKL-2000
    Structure Solution HKL-3000:SHELXC/D/E, MLPHARE, DM, ARP/wARP, SOLVE, RESOLVE, CCP4
    Structure Refinement REFMAC 5.6.0117
     
    Software
    refinement REFMAC version: 5.6.0117
    model building CCP4
    model building RESOLVE
    model building SOLVE
    model building ARP/wARP
    model building DM
    model building MLPHARE
    model building HKL-3000:SHELXC/D/E
    data collection MD2